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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11694 | |||||||||
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Title | Human pre-Bact-1 spliceosome core structure | |||||||||
![]() | Sharpened/masked map for pre-Bact-1 core structure. | |||||||||
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Function / homology | ![]() microfibril / regulation of retinoic acid receptor signaling pathway / WW domain binding / regulation of vitamin D receptor signaling pathway / nuclear retinoic acid receptor binding / transcription elongation factor activity / Prp19 complex / positive regulation of androgen receptor activity / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome ...microfibril / regulation of retinoic acid receptor signaling pathway / WW domain binding / regulation of vitamin D receptor signaling pathway / nuclear retinoic acid receptor binding / transcription elongation factor activity / Prp19 complex / positive regulation of androgen receptor activity / RNA splicing, via transesterification reactions / U2-type catalytic step 1 spliceosome / mRNA cis splicing, via spliceosome / positive regulation by host of viral transcription / U2-type precatalytic spliceosome / U2-type spliceosomal complex / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / RNA polymerase binding / U2-type catalytic step 2 spliceosome / ubiquitin-like protein conjugating enzyme binding / Notch binding / positive regulation of mRNA splicing, via spliceosome / Regulation of gene expression in late stage (branching morphogenesis) pancreatic bud precursor cells / RUNX3 regulates NOTCH signaling / NOTCH4 Intracellular Domain Regulates Transcription / positive regulation of protein targeting to mitochondrion / NOTCH3 Intracellular Domain Regulates Transcription / Cajal body / positive regulation of neurogenesis / nuclear androgen receptor binding / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of G1/S transition of mitotic cell cycle / precatalytic spliceosome / retinoic acid receptor signaling pathway / Notch-HLH transcription pathway / positive regulation of transforming growth factor beta receptor signaling pathway / Formation of paraxial mesoderm / negative regulation of transcription elongation by RNA polymerase II / mRNA Splicing - Minor Pathway / SMAD binding / protein localization to nucleus / spliceosomal tri-snRNP complex assembly / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / positive regulation of transcription elongation by RNA polymerase II / pre-mRNA intronic binding / cellular response to retinoic acid / U1 snRNA binding / transcription coregulator activity / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / nuclear receptor coactivator activity / response to cocaine / nuclear receptor binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / spliceosomal complex / protein modification process / NOTCH1 Intracellular Domain Regulates Transcription / Pre-NOTCH Transcription and Translation / fibrillar center / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / nuclear matrix / mRNA splicing, via spliceosome / mRNA processing / cellular response to xenobiotic stimulus / rRNA processing / protein tag activity / transcription corepressor activity / cellular response to tumor necrosis factor / single-stranded DNA binding / nuclear membrane / cellular response to lipopolysaccharide / transcription coactivator activity / RNA polymerase II-specific DNA-binding transcription factor binding / nuclear body / nuclear speck / intracellular membrane-bounded organelle / negative regulation of DNA-templated transcription / GTPase activity / centrosome / regulation of transcription by RNA polymerase II / chromatin / GTP binding / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Townsend C / Kastner B / Leelaram MN / Bertram K / Stark H / Luehrmann R | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism of protein-guided folding of the active site U2/U6 RNA during spliceosome activation. Authors: Cole Townsend / Majety N Leelaram / Dmitry E Agafonov / Olexandr Dybkov / Cindy L Will / Karl Bertram / Henning Urlaub / Berthold Kastner / Holger Stark / Reinhard Lührmann / ![]() Abstract: Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway ...Spliceosome activation involves extensive protein and RNA rearrangements that lead to formation of a catalytically active U2/U6 RNA structure. At present, little is known about the assembly pathway of the latter and the mechanism whereby proteins aid its proper folding. Here, we report the cryo-electron microscopy structures of two human, activated spliceosome precursors (that is, pre-B complexes) at core resolutions of 3.9 and 4.2 angstroms. These structures elucidate the order of the numerous protein exchanges that occur during activation, the mutually exclusive interactions that ensure the correct order of ribonucleoprotein rearrangements needed to form the U2/U6 catalytic RNA, and the stepwise folding pathway of the latter. Structural comparisons with mature B complexes reveal the molecular mechanism whereby a conformational change in the scaffold protein PRP8 facilitates final three-dimensional folding of the U2/U6 catalytic RNA. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 14.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 32.5 KB 32.5 KB | Display Display | ![]() |
Images | ![]() | 33.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7abfMC ![]() 7aavC ![]() 7abgC ![]() 7abhC ![]() 7abiC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data #1: Motion-corrected micrographs (without dose-weighting) of human pre-Bact spliceosome [micrographs - single frame] Data #2: Motion-corrected micrographs (with dose-weighting) of human pre-Bact spliceosome [micrographs - single frame]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Sharpened/masked map for pre-Bact-1 core structure. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.16 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : pre-Bact-1 spliceosomal complex
+Supramolecule #1: pre-Bact-1 spliceosomal complex
+Supramolecule #2: pre-Bact-1 spliceosomal complex
+Supramolecule #3: MINX M3 RNA
+Macromolecule #1: Protein BUD31 homolog
+Macromolecule #2: Pre-mRNA-splicing factor 38A
+Macromolecule #3: Pre-mRNA-processing-splicing factor 8
+Macromolecule #4: 116 kDa U5 small nuclear ribonucleoprotein component
+Macromolecule #5: Zinc finger matrin-type protein 2
+Macromolecule #6: Ubiquitin-like protein 5
+Macromolecule #7: Spliceosome-associated protein CWC15 homolog
+Macromolecule #10: WW domain-binding protein 11
+Macromolecule #11: SNW domain-containing protein 1
+Macromolecule #12: Pleiotropic regulator 1
+Macromolecule #14: Microfibrillar-associated protein 1
+Macromolecule #15: Transcription elongation regulator 1
+Macromolecule #8: U5 small nuclear RNA
+Macromolecule #9: U6 small nuclear RNA
+Macromolecule #13: MINX M3 RNA
+Macromolecule #16: INOSITOL HEXAKISPHOSPHATE
+Macromolecule #17: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #18: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.9 |
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Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS |
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average exposure time: 1.0 sec. / Average electron dose: 2.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER / Details: cryoSPARC ab initio reconstruction |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 84539 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-7abf: |